# -*- coding: utf-8 -*-
# pylint:disable=invalid-name, logging-format-interpolation, logging-fstring-interpolation, line-too-long, dangerous-default-value, too-many-lines
"""Featurization functions for the oxidation state mining project. Wrapper around matminer"""
import logging
import os
import pickle
import warnings
from glob import glob
from pathlib import Path
from typing import Dict, List, Tuple, Union
import numpy as np
import pandas as pd
from ase.io import read
from matminer.featurizers.base import MultipleFeaturizer
from matminer.featurizers.site import CrystalNNFingerprint, GaussianSymmFunc
from matminer.utils.data import MagpieData
from pymatgen import Structure
from pymatgen.core import Element
from pymatgen.io.ase import AseAtomsAdaptor
from pymatgen.io.cif import CifParser
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from skmultilearn.model_selection import IterativeStratification
from .exclude import TO_EXCLUDE
from .featurizer_local_property import LocalPropertyStatsNew
from .utils import apricot_select, diff_to_18e, read_pickle
collectorlogger = logging.getLogger("FeatureCollector")
collectorlogger.setLevel(logging.INFO)
logging.basicConfig(format="%(filename)s: %(message)s", level=logging.INFO)
METAL_CENTER_FEATURES: List[str] = [
"column",
"row",
"valenceelectrons",
"diffto18electrons",
"sunfilled",
"punfilled",
"dunfilled",
]
GEOMETRY_FEATURES: List[str] = ["crystal_nn_fingerprint", "behler_parinello"]
CHEMISTRY_FEATURES: List[str] = ["local_property_stats"]
FEATURE_RANGES_DICT: Dict[str, List[Tuple[int, int]]] = {
"crystal_nn_fingerprint": [(0, 61)],
"crystal_nn_no_steinhardt": [(0, 33), (36, 37), (40, 41), (44, 46), (49, 61)],
"local_property_stats": [(61, 121)],
"column_differences": [(62, 63), (77, 78), (92, 93), (107, 108)],
"row_differences": [(63, 64), (78, 79), (93, 94), (108, 109)],
"electronegativity_differences": [(64, 65), (79, 80), (94, 95), (109, 110)],
"valence_differences": [(69, 70), (84, 85), (99, 100), (114, 115)],
"unfilled_differences": [(74, 75), (89, 90), (104, 105), (119, 120)],
"nsvalence_differences": [(65, 66), (79, 80), (95, 96), (110, 111)],
"behler_parinello": [(121, 129)],
"number": [(129, 130)],
"row": [(130, 131)],
"column": [(131, 132)],
"valenceelectrons": [(132, 133)],
"diffto18electrons": [(133, 134)],
"sunfilled": [(134, 135)],
"punfilled": [(135, 136)],
"dunfilled": [(136, 137)],
"random_column": [(137, 138)],
"optimized_feature_set": [
(0, 33),
(36, 37),
(40, 41),
(44, 46),
(49, 61),
(130, 131),
(131, 132),
(76, 90),
],
}
FEATURE_LABELS_ALL: List[str] = [
"wt CN_1",
"sgl_bd CN_1",
"wt CN_2",
"L-shaped CN_2",
"water-like CN_2",
"bent 120 degrees CN_2",
"bent 150 degrees CN_2",
"linear CN_2",
"wt CN_3",
"trigonal planar CN_3",
"trigonal non-coplanar CN_3",
"T-shaped CN_3",
"wt CN_4",
"square co-planar CN_4",
"tetrahedral CN_4",
"rectangular see-saw-like CN_4",
"see-saw-like CN_4",
"trigonal pyramidal CN_4",
"wt CN_5",
"pentagonal planar CN_5",
"square pyramidal CN_5",
"trigonal bipyramidal CN_5",
"wt CN_6",
"hexagonal planar CN_6",
"octahedral CN_6",
"pentagonal pyramidal CN_6",
"wt CN_7",
"hexagonal pyramidal CN_7",
"pentagonal bipyramidal CN_7",
"wt CN_8",
"body-centered cubic CN_8",
"hexagonal bipyramidal CN_8",
"wt CN_9",
"q2 CN_9",
"q4 CN_9",
"q6 CN_9",
"wt CN_10",
"q2 CN_10",
"q4 CN_10",
"q6 CN_10",
"wt CN_11",
"q2 CN_11",
"q4 CN_11",
"q6 CN_11",
"wt CN_12",
"cuboctahedral CN_12",
"q2 CN_12",
"q4 CN_12",
"q6 CN_12",
"wt CN_13",
"wt CN_14",
"wt CN_15",
"wt CN_16",
"wt CN_17",
"wt CN_18",
"wt CN_19",
"wt CN_20",
"wt CN_21",
"wt CN_22",
"wt CN_23",
"wt CN_24",
"local difference in MendeleevNumber",
"local difference in Column",
"local difference in Row",
"local difference in Electronegativity",
"local difference in NsValence",
"local difference in NpValence",
"local difference in NdValence",
"local difference in NfValence",
"local difference in NValence",
"local difference in NsUnfilled",
"local difference in NpUnfilled",
"local difference in NdUnfilled",
"local difference in NfUnfilled",
"local difference in NUnfilled",
"local difference in GSbandgap",
"local signed difference in MendeleevNumber",
"local signed difference in Column",
"local signed difference in Row",
"local signed difference in Electronegativity",
"local signed difference in NsValence",
"local signed difference in NpValence",
"local signed difference in NdValence",
"local signed difference in NfValence",
"local signed difference in NValence",
"local signed difference in NsUnfilled",
"local signed difference in NpUnfilled",
"local signed difference in NdUnfilled",
"local signed difference in NfUnfilled",
"local signed difference in NUnfilled",
"local signed difference in GSbandgap",
"maximum local difference in MendeleevNumber",
"maximum local difference in Column",
"maximum local difference in Row",
"maximum local difference in Electronegativity",
"maximum local difference in NsValence",
"maximum local difference in NpValence",
"maximum local difference in NdValence",
"maximum local difference in NfValence",
"maximum local difference in NValence",
"maximum local difference in NsUnfilled",
"maximum local difference in NpUnfilled",
"maximum local difference in NdUnfilled",
"maximum local difference in NfUnfilled",
"maximum local difference in NUnfilled",
"maximum local difference in GSbandgap",
"mimum local difference in MendeleevNumber",
"mimum local difference in Column",
"mimum local difference in Row",
"mimum local difference in Electronegativity",
"mimum local difference in NsValence",
"mimum local difference in NpValence",
"mimum local difference in NdValence",
"mimum local difference in NfValence",
"mimum local difference in NValence",
"mimum local difference in NsUnfilled",
"mimum local difference in NpUnfilled",
"mimum local difference in NdUnfilled",
"mimum local difference in NfUnfilled",
"mimum local difference in NUnfilled",
"mimum local difference in GSbandgap",
"G2_0.05",
"G2_4.0",
"G2_20.0",
"G2_80.0",
"G4_0.005_1.0_1.0",
"G4_0.005_1.0_-1.0",
"G4_0.005_4.0_1.0",
"G4_0.005_4.0_-1.0",
"number",
"row",
"column",
"valenceelectrons",
"diffto18electrons",
"sunfilled",
"punfilled",
"dunfilled",
"random_column",
]
SELECTED_RACS: List[str] = [
"D_mc-I-0-all",
"D_mc-I-1-all",
"D_mc-I-2-all",
"D_mc-I-3-all",
"D_mc-S-0-all",
"D_mc-S-1-all",
"D_mc-S-2-all",
"D_mc-S-3-all",
"D_mc-T-0-all",
"D_mc-T-1-all",
"D_mc-T-2-all",
"D_mc-T-3-all",
"D_mc-Z-0-all",
"D_mc-Z-1-all",
"D_mc-Z-2-all",
"D_mc-Z-3-all",
"D_mc-chi-0-all",
"D_mc-chi-1-all",
"D_mc-chi-2-all",
"D_mc-chi-3-all",
"mc-I-0-all",
"mc-I-1-all",
"mc-I-2-all",
"mc-I-3-all",
"mc-S-0-all",
"mc-S-1-all",
"mc-S-2-all",
"mc-S-3-all",
"mc-T-0-all",
"mc-T-1-all",
"mc-T-2-all",
"mc-T-3-all",
"mc-Z-0-all",
"mc-Z-1-all",
"mc-Z-2-all",
"mc-Z-3-all",
"mc-chi-0-all",
"mc-chi-1-all",
"mc-chi-2-all",
"mc-chi-3-all",
]
__all__ = [
"GetFeatures",
"FeatureCollector",
"METAL_CENTER_FEATURES",
"GEOMETRY_FEATURES",
"CHEMISTRY_FEATURES",
"SELECTED_RACS",
"FEATURE_LABELS_ALL",
"FEATURE_RANGES_DICT",
"featurize",
"get_feature_names",
]
DEFAULT_FEATURE_SET = (
["local_property_stats"]
+ [
"column",
"row",
"valenceelectrons",
"diffto18electrons",
"sunfilled",
"punfilled",
"dunfilled",
]
+ ["crystal_nn_no_steinhardt"]
)
def _choose_cutoff(structure):
"""Cutoff is the longest diagonal,
re-using https://pymatgen.org/_modules/pymatgen/analysis/local_env.html"""
corners = [[1, 1, 1], [-1, 1, 1], [1, -1, 1], [1, 1, -1]]
d_corners = [
np.linalg.norm(structure.lattice.get_cartesian_coords(c)) for c in corners
]
max_cutoff = max(d_corners) + 0.01
return max_cutoff
[docs]def get_feature_names(selected_features: List[str], offset: int = 0) -> List[str]:
"""Given a set of selected feature categories, return all feature names
Args:
selected_features (List[str]): feature categories
offset (int, optional): To offset the feature ranges,
to be used with RACs. Defaults to 0.
Returns:
List[str]: list of feature names
"""
featurenames = []
# RACs are naturally considered
for feature in selected_features:
featureranges = FEATURE_RANGES_DICT[feature]
for featurerange in featureranges:
lower, upper = featurerange
# adding the offset to account for RACS from seperate file
# that are added at the start of the feature list
lower += offset
upper += offset
featurenames.extend(FEATURE_LABELS_ALL[lower:upper])
return featurenames
[docs]def featurize(
structure: Structure, featureset: List[str] = DEFAULT_FEATURE_SET
) -> Union[np.array, list, list]:
"""Finds metals in the structure, featurizes the metal sites and collects the features
Args:
structure (pymatgen.Structure): Structure to featurize
featureset (List[str]): Features to be used in the final output
Returns:
Union[np.array, list, list]: [description]
"""
# structure = _round_structure(structure)
get_feat = GetFeatures(structure, "")
features = get_feat.return_features()
metal_indices = get_feat.metal_indices
X = []
feat_dict_list = FeatureCollector.create_dict_for_feature_table_from_dict(features)
for feat_dict in feat_dict_list:
X.append(feat_dict["feature"])
X = np.vstack(X)
(
X,
_,
) = FeatureCollector._select_features_return_names( # pylint:disable=protected-access
featureset, X
)
metals = [site.species_string for site in get_feat.metal_sites]
return X, metal_indices, metals
[docs]class GetFeatures: # pylint:disable=too-many-instance-attributes
"""Featurizer"""
[docs] def __init__(self, structure: Structure, outpath: Union[str, Path]):
"""Generates features for a structures
Args:
structure (Structure): Pymatgen Structure object
outpath (Union[str, Path]): path to which the features will be dumped
Returns:
"""
featurizelogger = logging.getLogger("Featurize")
featurizelogger.setLevel(logging.INFO)
logging.basicConfig(
format="%(filename)s: %(message)s",
level=logging.INFO,
)
self.outpath = outpath
if (
(outpath != "")
and (outpath is not None)
and (not os.path.exists(self.outpath))
):
os.mkdir(self.outpath)
self.logger = featurizelogger
self.path = None
self.structure = structure
self.spacegroup_analyzer = SpacegroupAnalyzer(structure)
self.symmetrized_structure = (
self.spacegroup_analyzer.get_symmetrized_structure()
)
self.metal_sites = []
self.metal_indices = []
self.features = []
if self.path is not None:
self.outname = os.path.join(
self.outpath, "".join([Path(self.path).stem, ".pkl"])
)
else:
self.outname = os.path.join(
self.outpath,
"".join([self.structure.formula.replace(" ", "_"), ".pkl"]),
)
self._cutoff = 35
@property
def cutoff(self):
"""Chose a cutoff for a given structure"""
try:
return _choose_cutoff(self.structure)
except Exception: # pylint: disable=broad-except
return self._cutoff
@property
def featurizer(self):
"""Return the featurizer (with the suitable cutoff)"""
cutoff = self.cutoff
return MultipleFeaturizer(
[
CrystalNNFingerprint.from_preset("ops", search_cutoff=cutoff),
LocalPropertyStatsNew.from_preset("interpretable", cutoff=cutoff),
GaussianSymmFunc(),
]
)
[docs] @classmethod
def from_file(
cls, structurepath: Union[str, Path], outpath: Union[str, Path]
) -> object:
"""Construct a featurizer class from path to structure
and an output path
Args:
structurepath (Union[str, Path]): Path to structure file
outpath (Union[str, Path]): Path to which the outputs should be written.
Returns:
object: Instance of the GetFeatures class
"""
s = GetFeatures._read_safe(structurepath)
featureclass = cls(s, outpath)
featureclass.path = structurepath
featureclass.outname = os.path.join(
featureclass.outpath, "".join([Path(featureclass.path).stem, ".pkl"])
)
return featureclass
[docs] @classmethod
def from_string(cls, structurestring: str, outpath: Union[str, Path]) -> object:
"""Constructor for the webapp, using a string of a structure file,
e.g., a CIF
Args:
structurestring (str): Fileconent of a CIF as string
outpath (Union[str, Path]): Path to which the output should be written.
Raises:
ValueError: In case the CIF could not be parsed
Returns:
object: Instance of GetFeatures
"""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
try:
cp = CifParser.from_string(structurestring)
s = cp.get_structures()[0]
except Exception as execp:
raise ValueError("Pymatgen could not parse ciffile") from execp
else:
return cls(s, outpath)
@staticmethod
def _read_safe(path: Union[str, Path]):
"""Fail early
Returns:
bool: True if check ok (if pymatgen can load structure)
"""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
try:
atoms = read(path)
structure = AseAtomsAdaptor.get_structure(
atoms
) # ase parser is a bit more robust
return structure
except Exception as execpt: # pylint: disable=broad-except
raise ValueError("Could not read structure") from execpt
def _get_metal_sites(self):
"""Stores all metal sites of structure to list"""
for idx, site in enumerate(self.structure):
if site.species.elements[0].is_metal:
self.metal_sites.append(site)
self.metal_indices.append(idx)
def _get_feature_vectors(self, site):
"""Runs matminer on one site"""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
X = self.featurizer.featurize(self.symmetrized_structure, site)
return X
def _dump_features(self):
"""Dumps all the features into one pickle file"""
with open(self.outname, "wb") as filehandle:
pickle.dump(list(self.features), filehandle)
[docs] def return_features(self) -> List[dict]:
"""Runs featurization and returns a list of dictionaries
Returns:
List[dict]: List of dictionaries of the form {"metal": , "feature", : , "coords"},
i.e features for one metal site
"""
self._get_metal_sites()
already_featurized = {}
try:
self.logger.debug(
"iterating over {} metal sites".format(len(self.metal_sites))
)
for idx, metal_site in enumerate(self.metal_sites):
feat = None
equivalent_sites = self.symmetrized_structure.find_equivalent_sites(
metal_site
)
for equivalent_site in equivalent_sites:
try:
feat = already_featurized[str(equivalent_site)]
except KeyError:
pass
else:
break
if feat is None:
feat = self._get_feature_vectors(self.metal_indices[idx])
self.features.append(
{
"metal": metal_site.species_string,
"feature": feat,
"coords": metal_site.coords,
}
)
already_featurized[str(metal_site)] = feat
except Exception as e: # pylint: disable=broad-except
self.logger.error("Could not featurize because of {}".format(e))
return self.features
def _run_featurization(self):
"""loops over sites if check ok"""
warnings.warn(
"This method is deprecated, and will be removed in a future release",
DeprecationWarning,
)
self._get_metal_sites()
try:
self.logger.info(
"iterating over {} metal sites".format(len(self.metal_sites))
)
for idx, metal_site in enumerate(self.metal_sites):
self.features.append(
{
"metal": metal_site.species_string,
"feature": self._get_feature_vectors(self.metal_indices[idx]),
"coords": metal_site.coords,
}
)
self._dump_features()
except Exception as e: # pylint: disable=broad-except
self.logger.error(
"could not featurize {} because of {}".format(self.path, e)
)
[docs]class FeatureCollector: # pylint:disable=too-many-instance-attributes,too-many-locals
"""convert features from a folder of pickle files to three
pickle files for feature matrix, label vector and names list."""
[docs] def __init__( # pylint:disable=too-many-arguments
self,
inpath: Union[str, Path] = None,
labelpath: Union[str, Path] = None,
outdir_labels: Union[str, Path] = "data/labels",
outdir_features: Union[str, Path] = "data/features",
outdir_helper: Union[str, Path] = "data/helper",
percentage_holdout: float = 0,
outdir_holdout: Union[str, Path] = None,
forbidden_picklepath: Union[str, Path] = None,
exclude_dir: Union[str, Path] = None,
selected_features: List[str] = CHEMISTRY_FEATURES
+ METAL_CENTER_FEATURES
+ ["crystal_nn_fingerprint"],
old_format: bool = False,
training_set_size: int = None,
racsfile: str = None,
selectedracs: List[str] = SELECTED_RACS,
drop_duplicates: bool = True,
):
"""Initializes a feature collector.
WARNING! The fingerprint selection function assumes that the full feature vector in the
pickle files has the columns as specified in FEATURE_LABELS_ALL
Keyword Arguments:
inpath (Union[str, Path]) -- path to directory with one pickle file per structure (default: None)
labelpath (Union[str, Path]) -- path to picklefile with labels (default: None)
outdir_labels (Union[str, Path]) -- path to output directory for labelsfile (default: "data/labels")
outdir_features (Union[str, Path]) -- path to output directory for featuresfile (default: "data/features")
outdir_helper (Union[str, Path]) -- path to output directory for helper files (feature names, structure names) (default: "data/helper")
percentage_holdout (float) -- precentage of all the data that should be put away as holdout
outdir_holdout (Union[str, Path]) -- directory into which the files for the holdout set are written (names, X and y)
forbidden_picklepath (Union[str, Path]) -- path to picklefile with list of forbidden CSD names (default: None)
exclude_dir (Union[str, Path]) -- path to directory with structure names are forbidden as well (default: None)
selected_features (List[str]) -- list of selected features. Available crystal_nn_fingerprint, cn, ward_prb, bond_orientational, behler_parinello
(default: ["crystal_nn_fingerprint","ward_prd","bond_orientational","behler_parinello"])
old_format (bool) -- if True, it uses the old feature dictionary style (default: {True})
training_set_size (int) -- if set to an int, it set an upper limit of the number of training points and uses farthest point sampling to select them
racsfile (str) -- path to file with RACs (pd.DataFrame saved as csv)
selectedracs (List[str]) -- list of selected RACs
"""
self.inpath = inpath
self.labelpath = labelpath
self.outdir_labels = outdir_labels
self.outdir_features = outdir_features
self.outdir_helper = outdir_helper
self.selected_features = selected_features
for feature in self.selected_features:
if feature not in list( # pylint:disable=no-else-raise
FEATURE_RANGES_DICT.keys()
):
raise KeyError("Cannot understand {}".format(feature))
else:
collectorlogger.info("will collect %s", feature)
self.percentage_holdout = percentage_holdout
self.outdir_holdout = outdir_holdout
self.outdir_valid = None
self.old_format = old_format
self.training_set_size = training_set_size
self.picklefiles = glob(os.path.join(inpath, "*.pkl"))
self.forbidden_list = (
list(read_pickle(forbidden_picklepath))
if forbidden_picklepath is not None
else []
)
# clashing = read_pickle(
# "clashing_atoms.pkl"
# ) # clashing atoms as determined by Mohamad
# self.forbidden_list.extend(clashing)
self.forbidden_list.extend(TO_EXCLUDE)
# just be double sure that we drop the ones we want to test on out
if exclude_dir is not None:
all_to_exclude = [
Path(p).stem for p in glob(os.path.join(exclude_dir, "*.cif"))
]
self.forbidden_list.extend(all_to_exclude)
self.forbidden_list = set(self.forbidden_list)
# collectorlogger.info(
# f'initialized feature collector: {len(self.forbidden_list)} forbidden structures, {len(self.picklefiles)} files with features'
# )
self.x = None
self.y = None
self.names = None
self.x_test = None
self.y_test = None
self.names_test = None
self.x_valid = None
self.y_valid = None
self.names_valid = None
# RACs
self.racsdf = None
self.selected_racs = selectedracs
if (racsfile is not None) and (racsfile.endswith(".csv")):
collectorlogger.info(
"Using RACs, now reading them and adding them to the feature names"
)
collectorlogger.warning(
"Be carful, RACs and their implementation in this code are not thoroughly tested!"
)
self.racsdf = pd.read_csv(racsfile)
self.selected_features = list(self.selected_racs) + list(
self.selected_features
) # to get the correct ordering
for i, feature in enumerate(self.selected_racs):
FEATURE_RANGES_DICT[feature] = [(i, i + 1)]
# If we encode with only metal centre, we cannot drop duplicates
self.drop_duplicates = drop_duplicates
@staticmethod
def _select_features(
selected_features: List[str],
X: np.ndarray,
outdir_helper: Union[str, Path] = None,
offset: int = 0,
):
"""Selects the feature and dumps the names as pickle in the helper directory.
Offset to be used if RACs are used"""
to_hstack = []
featurenames = []
# RACs are naturally considered
for feature in selected_features:
featureranges = FEATURE_RANGES_DICT[feature]
for featurerange in featureranges:
lower, upper = featurerange
# adding the offset to account for RACS from seperate file
# that are added at the start of the feature list
lower += offset
upper += offset
to_hstack.append(X[:, lower:upper])
featurenames.extend(FEATURE_LABELS_ALL[lower:upper])
collectorlogger.debug("the feature names are %s", featurenames)
if outdir_helper is not None:
with open(os.path.join(outdir_helper, "feature_names.pkl"), "wb") as fh:
pickle.dump(featurenames, fh)
return np.hstack(to_hstack)
@staticmethod
def _select_features_return_names(
selected_features: List[str], X: np.ndarray, offset: int = 0
):
"""Selects the feature and dumps the names as pickle in the helper directory.
Offset to be used if RACs are used"""
to_hstack = []
featurenames = []
# RACs are naturally considered
for feature in selected_features:
featureranges = FEATURE_RANGES_DICT[feature]
for featurerange in featureranges:
lower, upper = featurerange
# adding the offset to account for RACS from seperate file
# that are added at the start of the feature list
lower += offset
upper += offset
to_hstack.append(X[:, lower:upper])
featurenames.extend(FEATURE_LABELS_ALL[lower:upper])
collectorlogger.debug("the feature names are %s", featurenames)
return np.hstack(to_hstack), featurenames
def _featurecollection(self) -> Tuple[np.array, np.array, list]:
"""
Runs the feature collection workflow.
Returns:
Tuple[np.array, np.array, list] -- numpy arrays of features and labels and list of names
"""
feature_list = FeatureCollector.create_feature_list(
self.picklefiles, self.forbidden_list, self.old_format
)
label_raw = read_pickle(self.labelpath)
# collectorlogger.info(f'found {len(label_raw)} labels')
label_list = FeatureCollector.make_labels_table(label_raw)
df = FeatureCollector._create_clean_dataframe(
feature_list, label_list, self.drop_duplicates
)
# shuffle dataframe for the next steps to ensure randomization
df = df.sample(frac=1).reset_index(drop=True)
# set offset of select features
offset = 0
if self.racsdf is not None:
offset = len(self.selected_racs)
df = FeatureCollector._merge_racs_frame(df, self.racsdf, self.selected_racs)
if self.percentage_holdout > 0:
# Make stratified split that also makes sure that no structure from the training set is in the test set
# This is important as the chmemical enviornments in structures can be quite similar (parsiomny principle of Pauling)
# We do not want to leak this information from training into test set
df["base_name"] = [n.strip("0123456789") for n in df["name"]]
df_name_select = df.drop_duplicates(subset=["base_name"])
df_name_select["numbers"] = (
df_name_select["metal"].astype("category").cat.codes
)
stratifier = IterativeStratification(
n_splits=2,
order=2,
sample_distribution_per_fold=[
self.percentage_holdout,
1.0 - self.percentage_holdout,
],
)
train_indexes, test_indexes = next(
stratifier.split(
df_name_select, df_name_select[["oxidationstate", "numbers"]]
)
)
train_names = df_name_select.iloc[train_indexes]
test_names = df_name_select.iloc[test_indexes]
train_names = list(train_names["base_name"])
test_names = list(test_names["base_name"])
df_train = df[df["base_name"].isin(train_names)]
df_test = df[df["base_name"].isin(test_names)]
x, self.y, self.names = FeatureCollector._get_x_y_names(df_train)
self.x = FeatureCollector._select_features(
self.selected_features, x, self.outdir_helper, offset
)
x_test, self.y_test, self.names_test = FeatureCollector._get_x_y_names(
df_test
)
self.x_test = FeatureCollector._select_features(
self.selected_features, x_test, self.outdir_helper, offset
)
else: # no seperate holdout set
x, self.y, self.names = FeatureCollector._get_x_y_names(df)
if (
self.training_set_size
): # perform farthest point sampling to selet a fixed number of training points
collectorlogger.debug(
"will now perform farthest point sampling on the feature matrix"
)
# Write one additional holdout set
assert self.training_set_size < len(df_train)
x, self.y, self.names = FeatureCollector._get_x_y_names(df_train)
x = FeatureCollector._select_features(
self.selected_features, x, self.outdir_helper, offset
)
# indices = greedy_farthest_point_samples(x, self.training_set_size)
indices = apricot_select(x, self.training_set_size)
_df_train = df_train
good_indices = _df_train.index.isin(indices)
df_train = _df_train[good_indices]
x, self.y, self.names = FeatureCollector._get_x_y_names(df_train)
df_validation = _df_train[~good_indices]
x_valid, self.y_valid, self.names_valid = FeatureCollector._get_x_y_names(
df_validation
)
self.x_valid = FeatureCollector._select_features(
self.selected_features, x_valid, self.outdir_helper, offset
)
self.x = FeatureCollector._select_features(
self.selected_features, x, self.outdir_helper, offset
)
collectorlogger.debug("the feature matrix shape is %s", self.x.shape)
[docs] def dump_featurecollection(self) -> None:
"""Collect features and write features, labels and names to seperate files"""
self._featurecollection()
FeatureCollector._write_output(
self.x,
self.y,
self.names,
self.outdir_labels,
self.outdir_features,
self.outdir_helper,
)
if self.x_test is not None:
FeatureCollector._write_output(
self.x_test,
self.y_test,
self.names_test,
self.outdir_holdout,
self.outdir_holdout,
self.outdir_holdout,
)
if self.x_valid is not None:
self.outdir_valid = os.path.join(self.outdir_holdout, "valid")
if not os.path.exists(self.outdir_valid):
os.makedirs(self.outdir_valid)
FeatureCollector._write_output(
self.x_valid,
self.y_valid,
self.names_valid,
self.outdir_valid,
self.outdir_valid,
self.outdir_valid,
)
def _return_featurecollection_train(self) -> Tuple[np.array, np.array, list]:
self._featurecollection()
return self.x, self.y, self.names
@staticmethod
def _selectracs(df: pd.DataFrame, columns: List[str] = SELECTED_RACS):
"""select the RACs columns from the dataframe"""
selected_columns = columns + [
"name",
"metal",
"coordinate_x",
"coordinate_y",
"coordinate_z",
]
return df[selected_columns]
@staticmethod
def _partial_match_in_name(name: str, forbidden_set: set) -> bool:
"""Tries to match also partial names, e.g. to ensure that MAHSUK01 or
MAHSUK02 is also matched when only MAHSUK is in the forbidden list"""
return any(name.rstrip("1234567890") in s for s in forbidden_set)
[docs] @staticmethod
def create_feature_list(
picklefiles: List[Union[str, Path]],
forbidden_list: list,
old_format: bool = True,
) -> list:
"""Reads a list of pickle files into dictionary
Arguments:
picklefiles (List[Union[str, Path]]) -- list of paths
forbidden_list (list) -- list of "forbidden" names (CSD naming convention),
that will not be used
old_format (bool) -- If true, it will assume that the pickle files are in old
"legacy" format. Default: True
Returns:
list -- parsed pickle contents
"""
collectorlogger.info("reading pickle files with features")
result_list = []
if not isinstance(forbidden_list, list):
forbidden_list = []
for pickle_file in picklefiles:
if not FeatureCollector._partial_match_in_name(
Path(pickle_file).stem, forbidden_list
):
if not old_format:
result_list.extend(
FeatureCollector.create_dict_for_feature_table(pickle_file)
)
else:
result_list.extend(
FeatureCollector._create_dict_for_feature_table(pickle_file)
)
else:
collectorlogger.info(
"{} is in forbidden list and will not be considered for X, y, names".format(
pickle_file
)
)
return result_list
[docs] @staticmethod
def make_labels_table(raw_labels: Dict[str, dict]) -> List[dict]:
"""Read raw labeling output into a dictionary format that can be used to construct pd.DataFrames
Warning: assumes that each metal in the structure has the same oxidation states as it takes the first
list element. Cases in which this is not fulfilled need to be filtered out earlier.
Arguments:
raw_labels (Dict[str, dict]) -- nested dictionary of {name: {metal: [oxidationstates]}}
Returns:
List[dict] -- list of dictionaries of the form [{'name':, 'metal':, 'oxidationstate':}]
"""
collectorlogger.info(
"converting raw list of features into list of site dictionaries"
)
result_list = []
for key, value in raw_labels.items():
for metal, oxstate in value.items():
result_list.append(
{"name": key, "metal": metal, "oxidationstate": oxstate[0]}
)
return result_list
@staticmethod
def _merge_racs_frame(
df_features: pd.DataFrame, df_racs: pd.DataFrame, selectedracs: List[str]
) -> pd.DataFrame:
"""Merges the selected RACs features to the other features"""
collectorlogger.info("Merging RACs into other features")
df_selected_racs = FeatureCollector._selectracs(df_racs, selectedracs)
df_selected_racs["coordinate_x"] = df_selected_racs["coordinate_x"].astype(
np.int32
)
df_selected_racs["coordinate_y"] = df_selected_racs["coordinate_y"].astype(
np.int32
)
df_selected_racs["coordinate_z"] = df_selected_racs["coordinate_z"].astype(
np.int32
)
df_features["coordinate_x"] = df_features["coordinate_x"].astype(np.int32)
df_features["coordinate_y"] = df_features["coordinate_y"].astype(np.int32)
df_features["coordinate_z"] = df_features["coordinate_z"].astype(np.int32)
df_merged = pd.merge(
df_features,
df_selected_racs,
left_on=["name", "metal", "coordinate_x", "coordinate_y", "coordinate_z"],
right_on=["name", "metal", "coordinate_x", "coordinate_y", "coordinate_z"],
)
df_merged.dropna(inplace=True)
df_merged = df_merged.loc[df_merged.astype(str).drop_duplicates().index]
new_feature_columns = []
for _, row in df_merged.iterrows():
new_feature_column = row["feature"]
racs = list(row[selectedracs])
racs.extend(new_feature_column)
new_feature_columns.append(racs)
df_merged.drop(columns=["feature"], inplace=True)
df_merged["feature"] = new_feature_columns
return df_merged
@staticmethod
def _create_clean_dataframe(
feature_list: list, label_list: list, drop_duplicates: bool = True
) -> pd.DataFrame:
"""Merge the features and the labels on names and metals and drop entry rows
Arguments:
feature_list (list) -- list of dictionaries of the features, names and metals
label_list (list) -- list of dicionaries with names, metals and labels
drop_duplicates (bool) -- drops duplicates if True
Returns:
pd.DataFrame -- Dataframe with each row describing a seperate metal site
"""
pd.options.mode.use_inf_as_na = True
collectorlogger.info("merging labels and features")
df_features = pd.DataFrame(feature_list)
df_labels = pd.DataFrame(label_list)
df_merged = pd.merge(
df_features,
df_labels,
left_on=["name", "metal"],
right_on=["name", "metal"],
)
collectorlogger.info(
"the length of the feature df is {} the length of the label df is {} and the merged one is {}".format(
len(df_features), len(df_labels), len(df_merged)
)
)
df_merged.dropna(inplace=True)
if drop_duplicates:
df_cleaned = df_merged.loc[
df_merged.astype(str).drop_duplicates().index
] # to be sure that we do not accidently have same examples in training and test set
else:
df_cleaned = df_merged
return df_cleaned
@staticmethod
def _get_x_y_names(df: pd.DataFrame) -> Tuple[np.array, np.array, list]:
"""Splits the columns of a dataframe into features, labels and names
Arguments:
df (pd.DataFrame) -- dataframe that in each row contains a full description of
a metal site with feature, oxidation state, metal and name
Returns:
Tuple[np.array, np.array, list] -- features, labels, names
"""
names = list(df["name"])
feature_list = df["feature"].values
features = np.array(feature_list)
labels = np.array(df["oxidationstate"])
return features, labels, names
[docs] @staticmethod
def create_dict_for_feature_table(picklefile: Union[str, Path]) -> List[dict]:
"""Reads in a pickle with features and returns a list of dictionaries with one dictionary per metal site.
Arguments:
picklefile (Union[str, Path]) -- path to pickle file
Returns:
List[dict] -- list of dicionary
"""
result = read_pickle(picklefile)
mpd = MagpieData()
result_list = []
for site in result:
e = Element(site["metal"])
valence_electrons = mpd.get_elemental_properties([e], "NValence")[0]
valence_to_donate = diff_to_18e(valence_electrons)
sunfilled = mpd.get_elemental_properties([e], "NsUnfilled")[0]
dunfilled = mpd.get_elemental_properties([e], "NdUnfilled")[0]
punfilled = mpd.get_elemental_properties([e], "NpUnfilled")[0]
metal_encoding = [
e.number,
e.row,
e.group,
valence_electrons,
valence_to_donate,
sunfilled,
punfilled,
dunfilled,
np.random.randint(1, 18),
]
features = list(site["feature"])
features.extend(metal_encoding)
result_dict = {
"metal": site["metal"],
"coordinate_x": int(site["coords"][0]),
"coordinate_y": int(site["coords"][1]),
"coordinate_z": int(site["coords"][2]),
"feature": features,
"name": Path(picklefile).stem,
}
if not np.isnan(np.array(features)).any():
result_list.append(result_dict)
return result_list
[docs] @staticmethod
def create_dict_for_feature_table_from_dict(d: dict) -> List[dict]:
"""Reads in a pickle with features and returns a list of dictionaries with one dictionary per metal site.
Arguments:
d (dict) -- dictionary
Returns:
List[dict] -- list of dicionary
"""
mpd = MagpieData()
result_list = []
for site in d:
e = Element(site["metal"])
valence_electrons = mpd.get_elemental_properties([e], "NValence")[0]
valence_to_donate = diff_to_18e(valence_electrons)
sunfilled = mpd.get_elemental_properties([e], "NsUnfilled")[0]
dunfilled = mpd.get_elemental_properties([e], "NdUnfilled")[0]
punfilled = mpd.get_elemental_properties([e], "NpUnfilled")[0]
metal_encoding = [
e.number,
e.row,
e.group,
valence_electrons,
valence_to_donate,
sunfilled,
punfilled,
dunfilled,
np.random.randint(1, 18),
]
features = list(site["feature"])
features.extend(metal_encoding)
result_dict = {
"metal": site["metal"],
"coordinate_x": int(site["coords"][0]),
"coordinate_y": int(site["coords"][1]),
"coordinate_z": int(site["coords"][2]),
"feature": features,
"name": "noname",
}
if not np.isnan(np.array(features)).any():
result_list.append(result_dict)
return result_list
@staticmethod
def _create_dict_for_feature_table(picklefile: Union[str, Path]) -> List[dict]:
"""Reads in a pickle with features and returns a list of dictionaries with one dictionary per metal site.
Arguments:
picklefile (Union[str, Path]) -- path to pickle file
Returns:
List[dict] -- list of dicionary
"""
warnings.warn(
"This method will be removed in the next major release",
DeprecationWarning,
)
result = read_pickle(picklefile)
result_list = []
for key, value in result.items():
e = Element(key)
metal_encoding = [e.number, e.row, e.group, np.random.randint(1, 18)]
features = list(value["feature"])
features.extend(metal_encoding)
result_dict = {
"metal": key,
"coords": value["coords"],
"feature": features,
"name": Path(picklefile).stem,
}
if not np.isnan(np.array(features)).any():
result_list.append(result_dict)
return result_list
@staticmethod
def _write_output( # pylint:disable=too-many-arguments
x: np.array,
y: np.array,
names: list,
outdir_labels: Union[str, Path],
outdir_features: Union[str, Path],
outdir_helper: Union[str, Path],
) -> None:
"""writes feature array, label array and name array into output files in outdir/datetime/{x,y}.npy and outdir/datetime/names.pkl
Arguments:
x (np.array) -- feature matrix
y (np.array) -- label vector
names (list) -- name list (csd identifiers)
outdir_labels (Union[str, Path]) -- directory into which labels are written
outdir_features (Union[str, Path]) -- directory into which features are written
outdir_helper (Union[str, Path]) -- directory into which names are written
"""
np.save(os.path.join(outdir_features, "features"), x)
np.save(os.path.join(outdir_labels, "labels"), y)
with open(os.path.join(outdir_helper, "names.pkl"), "wb") as picklefile:
pickle.dump(names, picklefile)
collectorlogger.info("stored features into labels and names into")
